Cell-based clustering using pixel clusters: Gaussian blur sigma=2, k=30, arcsinh

Heatmaps of pixel clusters x markers

Compare pixel clusering with cell clustering

Cell-based FlowSOM clustering using all pixel clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 5, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 44"

## [1] "Dropped clusters: 1,2,3,4,5,6,7,8,9,10,11,13,14,15,16,19,21,22,23,24,25,26,27,28,29,30,32,36,39,43,44,50,51,52,56,57,59,60,61,64,65,66,74,80"

Cell-based FlowSOM clustering using pixel hierarchical clusters

No transformation

Normalize by total (covert from count to frequency), arcsinh transform, 99.99% normalization

Drop pixel clusters that do not have at least one marker ranked in top 2, normalize by total, arcsinh, 99.99% normalization

## [1] "Number of dropped clusters: 6"

## [1] "Dropped clusters: 1,2,3,6,11,14"